2025-07-09 オークリッジ国立研究所（ORNL）
Water is the most prevalent component of biomolecular simulations — from protein ensembles to nucleic acids — and inaccurately simulating it can lead to errors for research results in biomolecular structure, function, dynamics and assembly. In a new study, ORNL researchers show how using a 2 (or more) femtosecond time step can cause such inaccurate water simulations. Credit: Dilip Asthagiri/ORNL, U.S. Dept. of Energy
＜関連情報＞
- https://www.ornl.gov/news/researchers-confirm-method-used-water-simulations-can-cause-errors
- https://pubs.rsc.org/en/content/articlelanding/2025/sc/d4sc08437c
- https://tiisys.com/blog/2024/05/08/post-137292/
液体水のp-V挙動と小タンパク質の水和自由エネルギー成分に対する等分散の失敗の結果 Consequences of the failure of equipartition for the p–V behavior of liquid water and the hydration free energy components of a small protein
Dilipkumar N. Asthagiri, Arjun Valiya Parambathu and Thomas L. Beck
Chemical Science Published:28 Mar 2025
DOI:https://doi.org/10.1039/D4SC08437C
Abstract
Earlier we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step δt ≤ 0.5 fs to ensure equipartition between translational and rotational modes. Here we extend that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examine integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small δt is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, and the dielectric constant, a measure of dipole moment fluctuations, are also seen to be sensitive to δt. Using the mean volume estimated from the NpT simulation, we examine the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to δt. In going from δt = 2 fs to δt = 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein.
